Predicting alpha diversity of African rain forests: models based on climate and satellite‐derived data do not perform better than a purely spatial model

Aim Our aim was to evaluate the extent to which we can predict and map tree alpha diversity across broad spatial scales either by using climate and remote sensing data or by exploiting spatial autocorrelation patterns. Location Tropical rain forest, West Africa and Atlantic Central Africa. Methods Alpha diversity estimates were compiled for trees with diameter at breast height ≥ 10 cm in 573 inventory plots. Linear regression (ordinary least squares, OLS) and random forest (RF) statistical techniques were used to project alpha diversity estimates at unsampled locations using climate data and remote sensing data [Moderate Resolution Imaging Spectroradiometer (MODIS), normalized difference vegetation index (NDVI), Quick Scatterometer (QSCAT), tree cover, elevation]. The prediction reliabilities of OLS and RF models were evaluated using a novel approach and compared to that of a kriging model based on geographic location alone. Results The predictive power of the kriging model was comparable to that of OLS and RF models based on climatic and remote sensing data. The three models provided congruent predictions of alpha diversity in well‐sampled areas but not in poorly inventoried locations. The reliability of the predictions of all three models declined markedly with distance from points with inventory data, becoming very low at distances > 50 km. According to inventory data, Atlantic Central African forests display a higher mean alpha diversity than do West African forests. Main conclusions The lower tree alpha diversity in West Africa than in Atlantic Central Africa may reflect a richer regional species pool in the latter. Our results emphasize and illustrate the need to test model predictions in a spatially explicit manner. Good OLS or RF model predictions from inventory data at short distance largely result from the strong spatial autocorrelation displayed by both the alpha diversity and the predictive variables rather than necessarily from causal relationships. Our results suggest that alpha diversity is driven by history rather than by the contemporary environment. Given the low predictive power of models, we call for a major effort to broaden the geographical extent and intensity of forest assessments to expand our knowledge of African rain forest diversity.     

Inventaire des moustiques (Diptera : Culicidae) des îles du sud-ouest de l’océan Indien,Madagascar excepté — Une revue critique

Inventory of the mosquitoes (Diptera: Culicidae) of the islands of southwestern Indian Ocean, Madagascar excluded – A Critical Review. The biodiversity of mosquitoes in the islands of southwestern Indian Ocean is the concern of numerous publications. Here, we propose a synthetic inventory and the analysis of the mosquito diversity, based on the available literature. A comprehensive annotated checklist of mosquito species has been recently published on Madagascar; this is the reason why this land is excluded from our work. Studied area encompasses 28 tropical islands in the southern hemisphere: 4 islands in the Comoros archipelago, 5 Scattered Islands (îles Éparses), 5 in Mascarene, 11 in the Seychelles and 3 in the Chagos archipelago. In total, the mosquito list presents 73 valid species, of which 10 are Anophelinae and 63 Culicinae. The number of species that are distributed in these islands only is 19, i.e. 26%, which is a remarkable level for endemism. The richness in mosquito species in these islands is analysed through several aspects including geography, local speciation and natural or human dissemination. This updated inventory increases by 33% the number of known species by regard to the previous inventory published by Julvez & Mouchet in 1994. The historical responsibility of humans in the introduction of new mosquito species in these islands is strongly documented. For instance, the species with the highest distribution among islands are Aedes aegypti, Ae. albopictus and Culex quinquefasciatus. The islands belong to the afrotropical biogeographic area and, logically, the majority (63%) of mosquito species present phylogenetic affinities with continental Africa and/or Madagascar; interestingly, the number of species present in these islands and in Madagascar but absent in continental Africa is higher than the number of species present in these islands and in continental Africa but absent in Madagascar (respectively 12 and 2 species). Thanks to valuable increase in the sampling effort, our knowledge of the culicidian fauna is increasing in these islands that constitute indisputably hotspots of biodiversity.     

Distribution and ecology of the ephemeropterans of Tunisia (1). (Insecta, Ephemeroptera)

The study of 51 localities distributed throughout most of Tunisia has permitted the first establishment of a faunistic inventory of 11 species of Ephemeropterans (excluding Baetidae). 7 of these are newly recorded for Tunisia and one is new for North Africa. Species distributions depend essentially on chemical parameters (salinity, Cl-, Ca++, etc.) and on conductivity. Increases in the ionic concentration of the water quickly cause large decreases in population diversity, as is seen in eastern, central and southern waters. In Kroumirie, in the North West, the waters are less mineralized and so support a richer fauna. The species Caenis luctuosa possesses by far the greatest range of ecological tolerance. It is the most abundant and most frequent throughout the region, being followed by Ecdyonurus rothschildi. Distributional maps are established and the species' biogeographies and periods of flight are studied.     

Ecosystem classification and inventory maps as surrogates for ground beetle assemblages in boreal forest

Aims We compare performance of ecosystem classification maps and provincial forest inventory data derived from air photography in reflecting ground beetle (Coleoptera: Carabidae) biodiversity patterns that are related to the forest canopy mosaic. Our biodiversity surrogacy model based on remotely sensed tree canopy cover is validated against field-collected ground data.Methods We used a systematic sampling grid of 198 sites, covering 84 km 2 of boreal mixedwood forest in northwestern Alberta, Canada. For every site, we determined tree basal area, characterized the ground beetle assemblage and obtained corresponding provincial forest inventory and ecosystem classification information. We used variation partitioning, ordination and misclassification matrices to compare beetle biodiversity patterns explained by alternative databases and to determine model biases originating from air photo-interpretation.Important findings Ecosystem classification data performed better than canopy cover derived from forest inventory maps in describing ground beetle biodiversity patterns. The biodiversity surrogacy models based on provincial forest inventory maps and field survey generally detected similar patterns but inaccuracies in air photo-interpretation of relative canopy cover led to differences between the two models. Compared to field survey data, air photo-interpretation tended to confuse two Picea species and two Populus species present and homogenize stand mixtures. This generated divergence in models of ecological association used to predict the relationship between ground beetle assemblages and tree canopy cover. Combination of relative canopy cover from provincial inventory with other geo-referenced land variables to produce the ecosystem classification maps improved biodiversity predictive power. The association observed between uncommon surrogates and uncommon ground beetle species emphasizes the benefits of detecting these surrogates as a part of landscape management. In order to complement conservation efforts established in protected areas, accurate, high resolution, wide ranging and spatially explicit knowledge of landscapes under management is primordial in order to apply effective biodiversity conservation strategies at the stand level as required in the extensively harvested portion of the boreal forest. In development of these strategies, an in-depth understanding of vegetation is key.     

An inventory of all known specimens of the coelacanth Latimeria chalumnae,with comments on trends in the catches

Synopsis A list is presented of all known specimens of the coelacanth Latimeria chalumnae based on a survey of the literature and of museum, aquarium and university holdings. Details are given of the date, place, time and depth of capture, the name and age of the fisherman, the length, weight and sex of the fish, the first literature record, the method of preservation and the present location of specimens, if known. A new number is assigned to each specimen. At least 172 coelacanths are known to have been caught since 1938. The first coelacanth was caught off South Africa but all properly documented, subsequent specimens have been caught off the islands of Grand Comoro and Anjouan in the Comoros. An appeal is made to the Comoran authorities for each specimen that is caught to be made available for scientific study. Museum authorities are also encouraged to allow their specimens to be X-rayed or dissected so that vital information can be obtained on fecundity, foetal nutrition and dietary preferences. It is essential for the coelacanth conservation effort that this inventory is maintained by the Coelacanth Conservation Council.     

Analyzing floristic inventories with multiple maps

Spatial observations of plant occurrences contain a wealth of information on relations among species and on the relation between species and environmental conditions. Typically, inventory data of this kind are large co-occurrence matrices, and hence, direct ecological interpretations based on expert knowledge are often very difficult. Hitherto, ordination approaches have been used to construct a virtual ordination space (represented as one or multiple scatter plots) in which species that often co-occur are situated close together, whereas species that hardly co-occur are found far apart. In this study, we investigate a recently proposed ordination approach, multiple maps t-SNE, that constructs multiple, independent ordination spaces in order to reveal and visualize complementary structure in the data. We compare multiple maps t-SNE to several conventional ordination approaches, exploring a large inventory of vascular plant occurrences (FLORKART). Our results reveal that multiple maps t-SNE is well suited for the analysis of floristic inventories. In particular, multiple maps t-SNE uncovers the major dependencies of species co-occurrences on climate and soil biogeochemical preconditions.     

Alien flora of India: taxonomic composition, invasion status and biogeographic affiliations

The wide knowledge gaps in invasion biology research that exist in the developing world are crucial impediments to the scientific management and global policymaking on biological invasions. In an effort to fill such knowledge gaps, we present here an inventory of the alien flora of India, based on systematic reviews and rigorous analyses of research studies (ca. 190) published over the last 120 years (1890–2010 AD), and updated with field records of the last two decades. Currently, the inventory comprises of 1,599 species, belonging to 842 genera in 161 families, and constitutes 8.5% of the total Indian vascular flora. The three most species-rich families are Asteraceae (134 spp.), Papilionaceae (114 spp.) and Poaceae (106 spp.), and the three largest genera are Eucalyptus (25 spp.), Ipomoea (22 spp.), and Senna (21 spp.). The majority of these species (812) have no report of escaping from cultivation. Of the remaining subset of 787 species, which have either escaped from intentional cultivation, or spread after unintentional introduction, casuals are represented by 57 spp., casual/naturalised by 114 spp., naturalised by 257 spp., naturalised/invasive by 134 spp., and invasive by 225 spp. Biogeographically, more than one-third (35%) of the alien flora in India has its native ranges in South America, followed by Asia (21%), Africa (20%), Europe (11%), Australia (8%), North America (4%); and cryptogenic (1%). The inventory is expected to serve as the scientific baseline on plant invasions in India, with implications for conservation of global biodiversity.     

A physical map of the chromosome 12 centromere

While current sequencing efforts consider the detection of alpha satellite repeats as logical end points for map construction, detailed maps of most pericentromeric regions are lacking to confirm this hypothesis. Here we identify the different alpha satellite families present at the pericentromeric region of chromosome 12. The order, size and location of these repeats is established using radiation hybrid analysis, pulsed field gel analysis and FISH and the maps are integrated with current sequence information. For the different classes of alpha satellites present at the chromosome 12 centromere the paralogs in the human genome were mapped by FISH. Unique sequences flanking the alpha satellite repeats were identified, some of which are not represented in the current draft sequence. This mapping effort localises the different alpha satellite repeats within the pericentromeric region and anchors them in the current maps. The novel sequences identified may serve as the end point for the ongoing sequencing efforts.     

Malaria in Africa: vector species' niche models and relative risk maps

A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km). Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes). For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis) these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.     

The US Fish and Wildlife Service's National Wetlands Inventory Project

In 1974, the US Fish and Wildlife Service directed its Office of Biological Services to design and conduct an inventory of the Nation's wetlands. The mandate was to develop and disseminate a technically sound, comprehensive data base concerning the characteristics and extent of the Nation's wetlands. The purpose of this data base is to foster wise use of the Nation's wetlands and to expedite decisions that may affect this important resource. To accomplish this, state-of-the-art principles and methodologies pertaining to all aspects of wetland inventory were assimilated and developed by the newly formed project. By 1979, when the National Wetlands Inventory (NWI) Project became operational, it was clear that two very different kinds of information were needed. First, detailed wetland maps were needed for site-specific decisions. Second, national statistics developed through statistical sampling on the current status and trends of wetlands were needed in order to provide information to support the development or alteration of Federal programs and policies. The NWI has produced wetland maps (scale=1:24 000) for 74% of the conterminous United States. It has also produced wetland maps (scale=1:63 360) for 24% of Alaska. Nearly 9000 of these wetland maps, representing 16.7% of the continental United States, have been computerized (digitized). In addition to maps, the NWI has produced other valuable wetland products. These include a statistically-based report on the status and trends of wetlands that details gains and losses in United States wetlands that have occurred from the mid-1970's to the mid-1980's. Other wetland products include a list of wetland (hydric) soils, a national list of wetland plant species, wetland reports for certain individual States such as New Jersey and Florida, and a wetland values data base.     

How Well Are Malaria Maps Used to Design and Finance Malaria Control in Africa?

Introduction

Rational decision making on malaria control depends on an understanding of the epidemiological risks and control measures. National Malaria Control Programmes across Africa have access to a range of state-of-the-art malaria risk mapping products that might serve their decision-making needs. The use of cartography in planning malaria control has never been methodically reviewed.

Materials and Methods

An audit of the risk maps used by NMCPs in 47 malaria endemic countries in Africa was undertaken by examining the most recent national malaria strategies, monitoring and evaluation plans, malaria programme reviews and applications submitted to the Global Fund. The types of maps presented and how they have been used to define priorities for investment and control was investigated.

Results

91% of endemic countries in Africa have defined malaria risk at sub-national levels using at least one risk map. The range of risk maps varies from maps based on suitability of climate for transmission; predicted malaria seasons and temperature/altitude limitations, to representations of clinical data and modelled parasite prevalence. The choice of maps is influenced by the source of the information. Maps developed using national data through in-country research partnerships have greater utility than more readily accessible web-based options developed without inputs from national control programmes. Although almost all countries have stratification maps, only a few use them to guide decisions on the selection of interventions allocation of resources for malaria control.

Conclusion

The way information on the epidemiology of malaria is presented and used needs to be addressed to ensure evidence-based added value in planning control. The science on modelled impact of interventions must be integrated into new mapping products to allow a translation of risk into rational decision making for malaria control. As overseas and domestic funding diminishes, strategic planning will be necessary to guide appropriate financing for malaria control.     

Genetic variation in North Amerindian populations: the geography of gene frequencies

Ten-level synthetic gene frequency maps derived from a principal component analysis of seven polymorphic loci are displayed for a large sample of North Amerindian populations. These maps are useful for assessing population affinities over broad geographical regions and perhaps, as others have argued, for inferring recent migrations. The influence of European admixture is investigated by deleting highly admixed populations and regenerating the maps. In broad outline the resultant geographic patterning, while appearing more homogeneous, preserves many features of the maps that include the highly admixed samples--especially with respect to the Eskimo/non-Eskimo dichotomy. Further, in an effort to evaluate how varying the number of display levels affects patterning as well as interpretation, the maps were replotted at 5 and 20 levels. The 5-level maps are found to accentuate differences between the full data set and the less admixed data set, while the 20-level maps tend to obscure these differences.     

Additive partitioning of rarefaction curves: Removing the influence of sampling on species-diversity in vegetation surveys

Vegetation surveys collect species-diversity information, a potentially valuable ecological indicator. However, the number of species recorded by vegetation surveys is influenced by several factors including inherent species-diversity, sampling method and sampling effort. The process of rarefaction is commonly used to control for variation in sampling effort. We aimed to use a combination of rarefaction and additive partitioning to control for sampling effort and extract vegetation α-, β- and γ-diversity respectively. The study focused on the Stony Plains region of the South Australian rangelands. Vegetation quadrat survey data were collected for land condition monitoring and species inventory by two government agencies. The analysis revealed a strong residual influence of sampling effort on β- and γ-diversity after rarefaction, a finding not previously reported in the literature. A method was developed to model then remove the residual influence of sampling effort on β- and γ-diversity. Thus the method outlined in this paper allows for the extraction from standard vegetation survey data of α-, β- and γ-diversity and the concurrent removal of sampling effort influence. This method is transferable to any other region for which there is vegetation survey data.     

Modeling the potential distribution of the predator of honey bees,Palarus latifrons,in the Arabian deserts using Maxent and GIS

ObjectivesThe species Palarus latifrons (bee pirates) has been recorded in Saudi Arabia as an invasive species. This pest can destroy honey bee colonies under certain conditions. The origin of this species in Africa and it has a good ability to adapt to desert conditions. Studies on this species are very few but its current distribution in the Arabian deserts is mainly in the Arabian Gulf countries. This study presents maps for the possible expansion of this species to invade other desert areas in the Arabian countries’ under current and near-future conditions (2030).MethodsThis pest is a solitary insect with high activity during summer. It is hypothesized that summer conditions and especially temperature are the limiting factor for its distribution in the deserts. The analysis depended on generating maps based on temperatures during summer and based on two bioclimatic factors. Maxent and the geographical information system (GIS) were used to perform the analysis.Results and conclusionsAll maps showed the high ability of this pest to spread in the Gulf countries. In North Africa: south Egypt and Libya, and some parts of Algeria showed suitability for Palarus. The invasion of this pest towards North Africa can happen mostly due to trading activities with Gulf countries especially materials containing soil. Continues monitoring for the activity of Palarus in the risk areas is highly advised.     

Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation

Aim The aim of this study is to analyse the distribution pattern of the botanical collecting effort in Amazonia so that it can be accounted for when interpreting phytogeographical patterns such as inferred species ranges. We also develop a mechanistic and transparent method for taking into account the bias in collecting effort when estimating likelihoods of species occurrences. Location Amazonia, Neotropics. Methods We utilized electronic data sets of georeferenced herbarium collections (1,063,530 in total). We plotted collecting localities (68,246 in total) on maps overlaid with 1° and 0.5° square grids, and analysed collecting effort using a geographical information system (GIS). We also drew a map of Thiessen polygons, using collecting localities as polygon centres, to visualize collecting density in a scale‐independent way. We then created a ‘collecting activity landscape’ in which well‐collected areas appear as peaks and poorly studied areas as valleys. We demonstrate how this surface can be utilized when estimating species distributions. Results The data available to us confirm that botanical collecting activity is still severely biased in Amazonia. The uncollected area represents 43% of the total area of Amazonia, while another 28% is poorly collected and only 2% can be considered relatively well collected. The Thiessen polygon network represents an improvement in the presentation of collecting intensity compared with square grids. Main conclusions The maps of botanical collecting effort in the Neotropics should be used for visually correcting phytogeographical interpretations. With the help of GIS applications the observed spatial bias in collecting effort can be utilized in estimating the likelihood of occurrence of species in a repeatable manner. These estimates, in turn, can be used for various purposes in basic and applied science as well as in decision‐making. The biased collecting effort should, in the long run, be corrected by further field work in unexplored areas, which can be identified with the maps presented here.     

Spatiotemporal spread of Plasmodium falciparum mutations for resistance to sulfadoxine-pyrimethamine across Africa, 1990–2020

BackgroundSulfadoxine-pyrimethamine (SP) is recommended in Africa in several antimalarial preventive regimens including Intermittent Preventive Treatment in pregnant women (IPTp), Intermittent Preventive Treatment in infants (IPTi) and Seasonal Malaria Chemoprevention (SMC). The effectiveness of SP-based preventive treatments are threatened in areas where Plasmodium falciparum resistance to SP is high. The prevalence of mutations in the dihydropteroate synthase gene (pfdhps) can be used to monitor SP effectiveness. IPTi-SP is recommended only in areas where the prevalence of the pfdhps540E mutation is below 50%. It has also been suggested that IPTp-SP does not have a protective effect in areas where the pfdhps581G mutation, exceeds 10%. However, pfdhps mutation prevalence data in Africa are extremely heterogenous and scattered, with data completely missing from many areas.Methods and findingsThe WWARN SP Molecular Surveyor database was designed to summarize dihydrofolate reductase (pfdhfr) and pfdhps gene mutation prevalence data. In this paper, pfdhps mutation prevalence data was used to generate continuous spatiotemporal surface maps of the estimated prevalence of the SP resistance markers pfdhps437G, pfdhps540E, and pfdhps581G in Africa from 1990 to 2020 using a geostatistical model, with a Bayesian inference framework to estimate uncertainty. The maps of estimated prevalence show an expansion of the pfdhps437G mutations across the entire continent over the last three decades. The pfdhps540E mutation emerged from limited foci in East Africa to currently exceeding 50% estimated prevalence in most of East and South East Africa. pfdhps540E distribution is expanding at low or moderate prevalence in central Africa and a predicted focus in West Africa. Although the pfdhps581G mutation spread from one focus in East Africa in 2000, to exceeding 10% estimated prevalence in several foci in 2010, the predicted distribution of the marker did not expand in 2020, however our analysis indicated high uncertainty in areas where pfdhps581G is present. Uncertainty was higher in spatial regions where the prevalence of a marker is intermediate or where prevalence is changing over time.ConclusionsThe WWARN SP Molecular Surveyor database and a set of continuous spatiotemporal surface maps were built to provide users with standardized, current information on resistance marker distribution and prevalence estimates. According to the maps, the high prevalence of pfdhps540E mutation was to date restricted to East and South East Africa, which is reassuring for continued use of IPTi and SMC in West Africa, but continuous monitoring is needed as the pfdhps540E distribution is expanding. Several foci where pfdhps581G prevalence exceeded 10% were identified. More data on the pfdhps581G distribution in these areas needs to be collected to guide IPTp-SP recommendations. Prevalence and uncertainty maps can be utilized together to strategically identify sites where increased surveillance can be most informative. This study combines a molecular marker database and predictive modelling to highlight areas of concern, which can be used to support decisions in public health, highlight knowledge gaps in certain regions, and guide future research.     

Mapping genes for common diseases: the case for genetic (LD) maps

We examine the current effort to develop a haplotype map of the human genome and suggest an alternative approach which represents linkage disequilibrium patterns in the form of a metric LD map. LD maps have some of the useful properties of genetic linkage maps but have a much higher resolution which is optimal for SNP-based association mapping of common diseases. The studies that have been undertaken to date suggest that LD and recombination maps show some close similarities because of abundant, narrow, recombination hot spots. These hot spots are co-localised in all populations but, unlike linkage maps, LD maps differ in scale for different populations because of differences in population history. The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence.     

Preliminary inventory of parasitoids associated with fruit flies in mangoes,guavas, cashew pepper and wild fruit crops in Benin

Fruit flies are pests of great economic importance due to their quarantine pest status and losses recorded in West Africa. An inventory of parasitoids associated with fruit flies in mangoes, guavas, cashew, pepper and major wild fruit crops was carried out in northern-central Benin in 2005, 2006, and 2008. Tephritid parasitoids reared from field-collected fruits belonged to three families: Braconidae (97.2%), Eulophidae (1.6%) and Pteromalidae (1.2%). Fopius caudatus (Szépligeti) accounted for 73.8% of all the parasitoids and therefore was the most abundant and widely distributed parasitoid. The parasitism rate was 7.7%, with the highest recorded in wild fruit crop habitat. Ceratitis cosyra (Walker) (77%) was the fly host most commonly reared from fruits that produced F. caudatus. The recently introduced pest Bactrocera invadens Drew Tsuruta and White was rarely parasitized and only by Pachycrepoideus vindemmiae (Rondani) (Hymenoptera: Pteromalidae) at this time. This is the first report of the inventory of one native parasitoid species from B. invadens in Africa, especially in West Africa.